Supplementary Table S1: List of validated hits from N minus RAS screen
S.N.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Gene
Methyl CpG Binding Protein 2 (MECP2)
Orthodenticle Homeobox 2 (OTX2)
Target Of Myb1 (Chicken) (TOM1)
G Protein-Coupled Receptor 171 (GPR171)
Flotillin 2 (FLOT2)
Chromosome 12 Open Reading Frame 74 (C12ORF74)
Histone Cluster 1, H2bn (HIST1H2BN)
Histone Cluster 1, H3f (HIST1H3F)
Solute Carrier Family 25, Member 41 (SLC25A41)
Chimerin 1 (CHN1)
Zinc Finger Protein 658 (ZNF658)
Lipoxygenase Homology Domains 1 (LOXHD1)
Regulator Of G-Protein Signaling 3 (RGS3)
Chloride Channel, Voltage-Sensitive Kb (CLCNKB)
Calmodulin 3 (Phosphorylase Kinase, Delta) (CALM3)
Entrez Gene
ID
4204
5015
10043
29909
2319
338809
8341
8968
284427
1123
26149
125336
5998
1188
808
Supplementary Table S2: Amplicons in Human Cancer (from Broad Institute TCGA Copy
Number Portal)
Peak Region
chr7:55065906-55102668
chr8:128739771-128769210
chr11:69460105-69484581
chr17:37855834-37875909
chr19:30306820-30315735
chr12:69212831-69260428
chr3:169416569-169490229
chr12:58135796-58155222
chr11:70140426-70213455
chr1:150519259-150703005
chr3:181256573-181731927
chr11:77613200-77640847
chr8:38171486-38254058
chr5:1288615-1299329
chr4:55008314-55104469
chr12:25344325-25370603
chr8:41761807-41929152
chr15:99056932-99774542
chr1:204353015-204538342
chr12:889902-1041097
chr20:30203029-30315025
chr1:40377907-40416849
chr1:242980673-247812431
chr19:39770395-39892270
chr17:57922442-57943519
chrX:153016891-153342426
(MECP2 containing amplicon)
chr7:92173409-92556768
chr1:160989893-161115583
chr8:101324125-101642253
chr20:52156927-52364760
chr8:37492872-37529770
chr6:43638636-43987936
chr3:197077908-197335218
chr13:113757997-114302622
#Genes
in Peak
1
1
2
1
1
2
2
6
1
8
3
1
2
1
1
3
1
6
3
12
2
0
84
9
1
18
Residual Qvalue
0
1.74E-272
2.12E-222
1.22E-204
5.49E-183
1.07E-144
2.03E-124
3.76E-122
5.18E-118
3.65E-113
9.82E-81
1.45E-78
2.04E-71
1.40E-60
1.46E-51
2.82E-44
4.94E-41
2.14E-37
1.58E-36
9.28E-34
9.01E-33
7.80E-29
1.22E-28
1.27E-28
1.34E-27
1.21E-26
Overall
0.382
0.453
0.208
0.199
0.24
0.211
0.335
0.205
0.204
0.37
0.328
0.169
0.234
0.317
0.114
0.245
0.259
0.145
0.363
0.247
0.391
0.145
0.352
0.217
0.242
0.176
Focal
0.068
0.129
0.106
0.054
0.066
0.053
0.118
0.045
0.102
0.1
0.118
0.068
0.067
0.071
0.05
0.041
0.06
0.064
0.046
0.058
0.045
0.051
0.072
0.043
0.048
0.059
Highlevel
0.084
0.139
0.065
0.038
0.055
0.04
0.093
0.033
0.062
0.078
0.089
0.031
0.057
0.076
0.023
0.047
0.055
0.018
0.066
0.043
0.073
0.018
0.06
0.035
0.029
0.018
4
9
4
2
0
5
1
13
8.22E-26
2.07E-25
9.37E-25
3.87E-24
1.51E-23
1.62E-21
2.59E-21
1.20E-19
0.363
0.369
0.417
0.401
0.223
0.197
0.315
0.179
0.039
0.077
0.061
0.043
0.059
0.043
0.112
0.058
0.05
0.069
0.104
0.083
0.051
0.027
0.078
0.03
chr11:102266643-102488711
chr17:27148617-27422161
chr20:62187416-62219648
chr19:15338573-15408584
chr14:36544027-37264674
chr6:20396454-20522290
chr8:144939389-145147978
chr9:35654478-35737197
chr11:66980818-67054144
chr4:1778801-1816690
chr18:20358314-20503269
chr17:73466243-73637996
chr6:107198296-107289865
chr11:34639284-34838823
chr10:76501637-77227430
chr2:178085599-178160931
chr8:80714469-81835247
chr17:77765982-77821663
chr5:37909815-44676519
chr4:73903374-74158212
chr14:105197567-105318962
chr22:18613737-22139416
chr19:55547934-58878226
chr8:55091227-55382067
chr6:64084316-64402884
chr12:66217394-66241372
chr5:176445948-176904216
chr9:4894234-5591850
chr19:35494834-36225620
chr14:20501368-21697941
chr19:10238547-10877387
chr7:146690968-158383607
chr17:48773492-49002559
chr10:5507029-5769453
chr13:73907772-73972011
chr7:708774-1243749
chr6:11203906-11588708
chr2:60243955-63176269
chr3:13669693-13758663
3
14
39
2
9
1
12
10
3
2
1
8
2
1
10
4
5
3
52
2
7
90
147
1
2
2
15
8
37
66
28
112
7
4
0
22
2
21
2
1.99E-19
1.97E-18
1.61E-17
1.95E-17
2.45E-15
1.01E-14
1.55E-14
1.99E-13
2.88E-13
2.44E-12
1.35E-11
6.82E-11
1.13E-09
1.69E-09
2.01E-09
1.47E-08
3.48E-08
5.70E-07
5.95E-07
1.78E-06
2.49E-06
3.08E-06
5.70E-06
8.28E-06
1.45E-05
1.58E-05
1.60E-05
2.00E-05
4.83E-05
7.10E-05
2.28E-04
5.87E-04
9.47E-04
0.003
0.00339
0.00349
0.00387
0.0124
0.0347
0.134
0.185
0.397
0.194
0.144
0.205
0.424
0.138
0.176
0.107
0.143
0.258
0.105
0.127
0.107
0.163
0.385
0.256
0.288
0.095
0.14
0.14
0.192
0.349
0.153
0.197
0.166
0.126
0.229
0.144
0.176
0.339
0.218
0.167
0.156
0.375
0.203
0.193
0.115
0.035
0.048
0.056
0.04
0.043
0.037
0.105
0.044
0.072
0.042
0.036
0.07
0.024
0.033
0.035
0.043
0.041
0.072
0.038
0.039
0.045
0.038
0.045
0.045
0.038
0.037
0.052
0.03
0.047
0.049
0.034
0.045
0.031
0.037
0.031
0.046
0.043
0.031
0.033
0.019
0.018
0.079
0.028
0.019
0.029
0.108
0.019
0.022
0.016
0.022
0.027
0.015
0.014
0.013
0.013
0.082
0.024
0.061
0.014
0.013
0.014
0.017
0.067
0.015
0.026
0.015
0.019
0.035
0.014
0.021
0.04
0.02
0.022
0.029
0.045
0.026
0.014
0.01
chr8:115442722-118152629
9
0.0752
0.43
chr9:139822542-140366608
44
0.0981
0.143
chr2:113962850-114139862
2
0.102
0.16
chr10:123172835-123398895
1
0.117
0.096
chr13:27260341-28888798
23
0.146
0.135
chr7:116314195-116508848
2
0.156
0.346
Note: Q values (False Discovery Values) below 0.25 are considered significant
0.083
0.043
0.034
0.029
0.031
0.027
0.109
0.011
0.011
0.009
0.023
0.041
Supplementary Table S3: Cancer cell lines used in current study with their MECP2 expression
and RAS/MAPK/PI3K pathways mutation status (based on COSMIC, canSAR, ATCC, and CCLE
databases)
Cell lines
BREAST
MECP2 overexpressing cell lines:
BT549
MDAMB468
MDAMB453
BT20
MCF7
Cell lines with low MECP2:
ZR75-1
MDAMB231
T47D
HCC38
LUNG
MECP2 overexpressing cell lines:
NCI-H1755
NCI-H23
NCI-H1993
NCI-H2228
NCI-H2170
NCI-H2009
NCI-H522
NCI-H1563
Cell lines with low MECP2:
NCI-H1437
NCI-H1395
NCI-H838
NCI-H2347
OVARIAN
MECP2 overexpressing cell lines:
EFO21
IGROV1
SKOV3
RAS
mutation
Other relevant mutations
(in MAPK and PI3K pathways)
Wild-type
Wild-type
Wild-type
Wild-type
Wild-type
PTENV275X
PTENA72fsX5
PTENE307K; PIK3CAH1047R
PIK3CAP539R; PIK3CAH1047R
PIK3CAE545K
Wild-type
KRASG13D
Wild-type
Wild-type
PTENL108R
BRAFG464V; NF2E231*
PIK3CAH1047R
Wild-type
KRASG12C
Wild-type
Wild-type
Wild-type
KRASG12A
Wild-type
Wild-type
BRAFG468A
Wild-type
Wild-type
Wild-type
NRASQ61R
Wild-type
Wild-type
Wild-type
MET amplification
EML4-ALK fusion
BRAFG469A
PTENY155C; PIK3CAR38C; AKT2V198A
ERBB2 amplification; PIK3CAH1047R
CAOV3
OVCAR4
Cell lines with low MECP2:
OVCAR3
OVCAR5
OVCAR8
Wild-type
Wild-type
PTENW274G
Wild-type
KRASG12V
KRASP121H
CCNE1 amplification; AKT2 amplification
ERBB2G776V